I definitely agree that System Suitability does not substitute for Qualification (ask anyone who has taken our Troubleshooting courses!) --
-- but "Qualification" does not address general instrument cleaning issues. Just re-read your post:
Waters Qualification include baseline drift, S/N analysis, peak height analysis
there is nothing in that list that measures how clean the instrument is.
More to the point, there is no way to set an absolute standard for "clean"; it depends on what you are doing. As an example from my own experience, at one point in my career I was doing a lot of single-column ion chromatography (basically, ion-exchange separation with conductivity detection). HPLC-grade water gave an enormous (unsuitable) background. It turns out that the specification for water quality was based on UV cutoff; the water could (and did) have significant ionic contamination and still pass. Plain old DI water gave a much lower background, but would never have passed for UV detection.
When all is said and done, the instrument (and supplies) must be sufficiently clean for the purpose of the analysis (i.e., "suitable for the purpose").